Genetic Diversity and Population Structure of Ethiopian Sheep Populations Revealed by High-Density SNP Markers.

Zewdu Edea,Tadelle Dessie,Kwan-Suk Kim,Kyoung-Tag Do,Hailu Dadi

doi:10.3389/fgene.2017.00218

Zewdu Edea, Tadelle Dessie + Show 3 more

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https://doi.org/10.3389/fgene.2017.00218

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Abstract

Sheep in Ethiopia are adapted to a wide range of environments, including extreme habitats. Elucidating their genetic diversity is critical for improving breeding strategies and mapping quantitative trait loci associated with productivity. To this end, the present study investigated the genetic diversity and population structure of five Ethiopian sheep populations exhibiting distinct phenotypes and sampled from distinct production environments, including arid lowlands and highlands. To investigate the genetic relationships in greater detail and infer population structure of Ethiopian sheep breeds at the continental and global levels, we analyzed genotypic data of selected sheep breeds from the Ovine SNP50K HapMap dataset. All Ethiopian sheep samples were genotyped with Ovine Infinium HD SNP BeadChip (600K). Mean genetic diversity ranged from 0.29 in Arsi-Bale to 0.32 in Menz sheep, while estimates of genetic differentiation among populations ranged from 0.02 to 0.07, indicating low to moderate differentiation. An analysis of molecular variance revealed that 94.62 and 5.38% of the genetic variation was attributable to differences within and among populations, respectively. Our population structure analysis revealed clustering of five Ethiopian sheep populations according to tail phenotype and geographic origin—i.e., short fat-tailed (very cool high-altitude), long fat-tailed (mid to high-altitude), and fat-rumped (arid low-altitude), with clear evidence of admixture between long fat-tailed populations. North African sheep breeds showed higher levels of within-breed diversity, but were less differentiated than breeds from Eastern and Southern Africa. When African breeds were grouped according to geographic origin (North, South, and East), statistically significant differences were detected among groups (regions). A comparison of population structure between Ethiopian and global sheep breeds showed that fat-tailed breeds from Eastern and Southern Africa clustered together, suggesting that these breeds were introduced to the African continent via the Horn and migrated further south.

Highlights

In the Horn of Africa and especially in Ethiopia where the economy is predominantly agriculture-based, sheep and their products play a critical role in the livelihood of millions of farmers and pastoralists (Wilson, 2011)
The mean minor allele frequency (MAF) ranged from 0.21 for OAR 11, 12, 14, 2, and 24 to 0.23 for OAR 23. These were lower than the reported average value (0.255 ± 0.136) for New Zealand sheep breeds based on an analysis of 517,902 single nucleotide polymorphism (SNP) and those reported for Corriedale and Merino sheep (0.27), but were higher than the value observed in Creole sheep (Grasso et al, 2014)
45,723 fixed SNPs were shared by the five Ethiopian sheep populations; the common SNPs (≥0.10 and ≤0.5) accounted for 71.03% of the total and ranged from 58.03% in Adilo to 66.56% in Horro sheep

Summary

Introduction

In the Horn of Africa and especially in Ethiopia where the economy is predominantly agriculture-based, sheep and their products play a critical role in the livelihood of millions of farmers and pastoralists (Wilson, 2011). Sheep serve as a source of income, mutton, and manure; provides an economic buffer in the event of crop failures; and fulfill many other sociocultural functions. In some areas such as the cool alpine and arid lowlands where crop production is not a viable economic option, sheep production is the sole option for livelihood (Tibbo, 2006). Sheep are important for the national economy; indigenous populations have evolved in diverse and harsh environments in Ethiopia where they face disease and parasite burdens, feed shortage, and extreme temperatures These animals likely harbor gene variants uniquely adapted to specific environmental conditions that may not be present in commercial breeds. The economic and agricultural value of sheep is expected to increase as a result of climate change (Seo, 2008; Seo et al, 2010); genetic characterization of local breeds adapted to extreme environments using modern genomic tools can ensure the breeding of hardy sheep populations (Boettcher et al, 2015; Yang et al, 2016)

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